Taxonomic identification report

Sample ID: VE24-1351_COI

Department of Agriculture, Fisheries and Forestry logo

[analysis description + link to github repo]

Facility Hogwarts
Analyst John Doe
Analysis started 2025-05-03 01:28:01
Analysis completed 2025-05-03 01:28:01
Wall time 0:0:0 hours

Result overview

Inconclusive

Outcome: The analyst should attempt subjective species identification at the genus level.

Reasoning: [Flag 1B] 2-3 candidate species matched with high stringency (identity ≥ 98.5%).

Preliminary morphology ID confirmed? NA

Inconclusive taxonomic identity (Flag 1B) Sciaridae.

Taxa of interest detected? True

Flag 2A: Taxon of interest detected in candidate species

Flag 5.1A: The given locus for this taxon is well represented in reference database (>5 entries)

Flag 5.2B: 10-90% of related taxa have reference sequence(s) at the given locus

Sample details

Locus COI
Preliminary ID Sciaridae
Taxa of interest Lycoriella ingenua
Country Netherlands
Host Lilium bulbs
Sample ID VE24-1351_COI
Query DNA sequence

Analyst evaluation

Identification of candidate species

Flag 1B: The analyst should attempt subjective species identification at the genus level
2-3 candidate species matched with high stringency (identity ≥ 98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits have then been classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 31 3
MODERATE MATCH ≥ 93.5% NA NA
NO MATCH < 93.5%

Candidate species

Species Hits Identity E-value Database coverage
Bradysia impatiens 2 100.0% 0.0
Lycoriella ingenua 27 100.0% 0.0
Lycoriella mali 2 100.0% 0.0

Analyst evaluation

Taxa of interest (TOI)

This sections shows the taxa of interest (TOI) specified by the sample submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

Taxon of interest Match rank Match taxon Match species Match accession Match identity Database coverage
Lycoriella ingenua species Lycoriella ingenua Lycoriella ingenua PQ008449 1.0

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

Independent sources

Flag 4B: Reference sequence sources lack diversity and may therefore be unreliable
Reasoning: Matching sequence records for this species have only 1-5 independent sources (found 1 sources)

1 Independent Source

The matching reference sequences for this species have been annotated by 1 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
MK861019 False Katumanyane,A.
Kanzi,A.M.
Malan,A.P. 		Fungus gnats in South Africa Unpublished
MK861019 False Katumanyane,A.
Kanzi,A.M.
Malan,A.P. 		Direct Submission Submitted (30-APR-2019) Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lunnon and Herold Street, Hatfiled, Pretoria 0002, South Africa
MK861018 False Katumanyane,A.
Kanzi,A.M.
Malan,A.P. 		Fungus gnats in South Africa Unpublished
MK861018 False Katumanyane,A.
Kanzi,A.M.
Malan,A.P. 		Direct Submission Submitted (30-APR-2019) Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lunnon and Herold Street, Hatfiled, Pretoria 0002, South Africa
Show Hide 2 more publications...

Independent sources

Flag 4A: Reference sequences are from diverse sources and therefore likely to be reliable
Reasoning: Matching sequence records for this species are from >5 independent sources (found 11 sources)

11 Independent Sources

The matching reference sequences for this species have been annotated by 11 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
PQ008449 False Ma,L.
Lin,J. 		Direct Submission Submitted (11-JUL-2024) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
PQ069699 False Ma,L.
Lin,J. 		Direct Submission Submitted (24-JUL-2024) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
PQ066142 False Ma,L.
Lin,J. 		Direct Submission Submitted (24-JUL-2024) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
PQ069630 False Ma,L.
Lin,J. 		Direct Submission Submitted (24-JUL-2024) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
PQ069628 False Ma,L.
Lin,J. 		Direct Submission Submitted (24-JUL-2024) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
Show Hide 3 more publications...

Source 2

Hit accession Automated Authors Title Journal
JN378570 False Shin,S.
Jung,S.
Lee,H.
Lee,S. 		Molecular identification of dipteran pests (Diptera: Sciaroidea) from shiitake mushroom Mol Ecol Resour 13 (2), 200-209 (2013)
JN378570 False Shin,S.
Lee,H.
Jung,S.
Lee,S. 		Direct Submission Submitted (20-JUL-2011) Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea

Source 3

Hit accession Automated Authors Title Journal
KX360302 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360302 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360295 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360295 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360299 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360299 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360301 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360301 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360300 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360300 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360292 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360292 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360315 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360315 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
KX360291 False Ye,L.
Leng,R.
Huang,J. 		Review of three greenhouse pest species of Black Fungus Gnats (Diptera:Sciaridae) from China Unpublished
KX360291 False Ye,L.
Leng,R.
Huang,J. 		Direct Submission Submitted (06-JUN-2016) Department of Forestry Protection, Zhejiang A & F University, Lin'an, Hangzhou, Zhejiang 311300, China
Show Hide 14 more publications...

Source 4

Hit accession Automated Authors Title Journal
FN868635 False Andrew King,R.
Moreno-Ripoll,R.
Agusti,N.
Shayler,S.P.
Bell,J.R.
Bohan,D.A.
Symondson,W.O. 		Multiplex reactions for the molecular detection of predation on pest and nonpest invertebrates in agroecosystems Mol Ecol Resour 11 (2), 370-373 (2011)
FN868635 False King,A. Direct Submission Submitted (19-MAY-2010) King A., School of Biosciences, University of Exeter, Stocker Road, EX4 4QD, UNITED KINGDOM

Source 5

Hit accession Automated Authors Title Journal
OR352396 False Yang,F.
Liu,H. 		A rapid multiplex PCR assay for the identification of black fungus gnats (Diptera: Sciaridae) and its application to larvae in mushrooms Unpublished
OR352396 False Yang,F.
Liu,H. 		Direct Submission Submitted (26-JUL-2023) Youth Research Group, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, No. 9, Shuguang Garden Middle Road, Beijing 100097, China
OR690424 False Yang,F.
Liu,H. 		Direct Submission Submitted (18-OCT-2023) Youth Research Group, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, No. 9, Shuguang Garden Middle Road, Beijing 100097, China
Show Hide 1 more publication...

Source 6

Hit accession Automated Authors Title Journal
MT252095 False Karademir,G.K.
Yildirim,A.
Inci,A.
Tuncbilek,A.S. 		Molecular Characterization of Lycoriella ingenua Lineges in Central Anatolia Region of Turkey Unpublished
MT252095 False Karademir,G.K.
Yildirim,A.
Inci,A.
Tuncbilek,A.S. 		Direct Submission Submitted (27-MAR-2020) Parasitology, Erciyes University Faculty of Veterinary Medicine, Talas, Kayseri 38039, Turkey

Source 7

Hit accession Automated Authors Title Journal
LC278318 False Arimoto,M.
Uesugi,R.
Hinomoto,N.
Sueyoshi,M.
Yoshimatsu,S. 		Molecular marker to identify the fungus gnat, Bradysia sp. (Diptera: Sciaridae), a new pest of Welsh onion and carrot in Japan Appl. Entomol. Zool. (Jpn.) 53, 419-424 (2018)
LC278318 False Arimoto,M.
Uesugi,R.
Hinomoto,H. 		Direct Submission Submitted (15-JUN-2017) Contact:Makoto Arimoto Central Region Agricultural Research Center, NARO, Division of Applied Entomology and Zoology; 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan URL :http://www.naro.affrc.go.jp/english/narc/index.html

Source 8

Hit accession Automated Authors Title Journal
OR251912 False Ma,L.
Qu,S.
Lin,J. 		Investigation of main fungus pests on Auricularia and screening of insecticides Unpublished
OR251912 False Ma,L.
Qu,S.
Lin,J. 		Direct Submission Submitted (11-JUL-2023) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
OR253027 False Ma,L.
Qu,S.
Lin,J. 		Investigation of main fungus pests on Auricularia and screening of insecticides Unpublished
OR253027 False Ma,L.
Qu,S.
Lin,J. 		Direct Submission Submitted (11-JUL-2023) Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing 210014, China
Show Hide 2 more publications...

Source 9

Hit accession Automated Authors Title Journal
MZ021517 False Hassan,A.A.
Al-Qaissi,A.R. 		The first record of the mushroom flies Megaselia halterata and Lycoriella ingenua in Iraq and the production of environmentally friendly attractants for these insect traps Unpublished
MZ021517 False Hassan,A.A.
Al-Qaissi,A.R. 		Direct Submission Submitted (24-APR-2021) Plant protection, Tikrit university, 73, Tikrit, Salah Aldin 00964, Iraq

Source 10

Hit accession Automated Authors Title Journal
MG291873 False Dewaard,J.R. BIOUG Archive GGBN Data Release Unpublished
MG291873 False Dewaard,J.R. Direct Submission Submitted (30-OCT-2017) Collections, Centre for Biodiversity Genomics, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
MG292424 False Dewaard,J.R. BIOUG Archive GGBN Data Release Unpublished
MG292424 False Dewaard,J.R. Direct Submission Submitted (30-OCT-2017) Collections, Centre for Biodiversity Genomics, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
MG159463 False Dewaard,J.R. BIOUG Archive GGBN Data Release Unpublished
MG159463 False Dewaard,J.R. Direct Submission Submitted (11-OCT-2017) Collections, Centre for Biodiversity Genomics, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
Show Hide 4 more publications...

Source 11

Hit accession Automated Authors Title Journal
KR746145 False Hebert,P.D.
Ratnasingham,S.
Zakharov,E.V.
Telfer,A.C.
Levesque-Beaudin,V.
Milton,M.A.
Pedersen,S.
Jannetta,P.
deWaard,J.R. 		Counting animal species with DNA barcodes: Canadian insects Philos. Trans. R. Soc. Lond., B, Biol. Sci. 371 (1702) (2016) In press
KR746145 False Hebert,P.D.N.
Ratnasingham,S.
Zakharov,E.V.
Dewaard,J.R. 		Direct Submission Submitted (15-MAY-2015) Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road EAST, Guelph, Ontario N1G2W1, Canada
KR761633 False Hebert,P.D.
Ratnasingham,S.
Zakharov,E.V.
Telfer,A.C.
Levesque-Beaudin,V.
Milton,M.A.
Pedersen,S.
Jannetta,P.
deWaard,J.R. 		Counting animal species with DNA barcodes: Canadian insects Philos. Trans. R. Soc. Lond., B, Biol. Sci. 371 (1702) (2016) In press
KR761633 False Hebert,P.D.N.
Ratnasingham,S.
Zakharov,E.V.
Dewaard,J.R. 		Direct Submission Submitted (15-MAY-2015) Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road EAST, Guelph, Ontario N1G2W1, Canada
Show Hide 2 more publications...

Independent sources

Flag 4B: Reference sequence sources lack diversity and may therefore be unreliable
Reasoning: Matching sequence records for this species have only 1-5 independent sources (found 1 sources)

1 Independent Source

The matching reference sequences for this species have been annotated by 1 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
AF319784 False Bae,J.S.
Kim,I.
Kim,S.R.
Jin,B.R.
Sohn,H.D. 		Mitochondrial DNA sequence variation of the mushroom pest flies, Lycoriella mali (Diptera: Sciaridae) and Coboldia fuscipes (Diptera: Scatopsidae) in Korea Appl. Entomol. Zool. (Jpn.) 36, 451-457 (2001)
AF319784 False Bae,J.-S. Direct Submission Submitted (08-NOV-2000) Dong-A University, 840 Hadan2-dong, Saha-gu, Busan, Korea
AF319811 False Bae,J.S.
Kim,I.
Kim,S.R.
Jin,B.R.
Sohn,H.D. 		Mitochondrial DNA sequence variation of the mushroom pest flies, Lycoriella mali (Diptera: Sciaridae) and Coboldia fuscipes (Diptera: Scatopsidae) in Korea Appl. Entomol. Zool. (Jpn.) 36, 451-457 (2001)
AF319811 False Bae,J.-S. Direct Submission Submitted (08-NOV-2000) Dong-A University, 840 Hadan2-dong, Saha-gu, Busan, Korea
Show Hide 2 more publications...

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net